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. 2016 Jan 29;11(1):e0147832. doi: 10.1371/journal.pone.0147832

Table 3. Comparison of RT-qPCR, RT-dPCR and RT-PCR array assays.

Characteristics of standard curves based on the RT-qPCR assays and limit of detection (LOD) of viral targets by RT-qPCR, by RT-dPCR and RT-PCR array assays. The differences between relative quantification (by RT-qPCR) and absolute quantification (by RT-dPCR) were indicated.

Virus Sample RT-qPCR (CFX96) RT-dPCR (FLUIDIGM) RT-PCR Array (FLUIDIGM)
Genome Type of sample Slope E R2 Range of detection (Ct value) LOD a LOD a log10(qPCR)-log10(dPCR) Difference between quantification type b LOD a log10(qPCR)-log10(PCR array)
Bocavirus DNA ss Plasmidic DNA -3.20 ± 0.20 106% 0.966 16.90–37.36 0.20 0.80 -0.60 0.17 1.00 -0.70
Parvovirus B19 DNA ss Plasmidic DNA -3.05 ± 0.14 113% 0.980 15.22–36.35 0.10 4.00 -1.60 -0.31 1.00 -1.00
Sapovirus RNA+ ss Transcript RNA -3.55 ± 0.29 91% 0.963 20.21–36.01 1.00E+01 4.00E+01 -0.60 0.89 1.00E+02 -1.00
Hepatitis E virus RNA+ ss Transcript RNA -3.49 ± 0.23 93% 0.972 19.91–38.15 1.00E+01 4.00E+01 -0.60 1.25 1.00E+02 -1.00
TBEV RNA+ ss Transcript RNA -3.10 ± 0.21 110% 0.970 21.66–37.54 1.00E+01 7.90E+01 -0.90 1.03 1.00E+04 -3.00
Aichi virus RNA+ ss Transcript RNA -3.34 ± 0.46 99% 0.933 27.18–36.53 1.00E+03 7.89E+02 0.10 1.32 1.00E+05 -2.00
229E RNA+ ss Transcript RNA -3.05 ± 0.37 113% 0.934 25.97–36.89 2.00E+01 3.95E+02 -1.30 1.64 1.00E+03 -1.70
HKU1 RNA+ ss Transcript RNA -3.41 ± 0.22 97% 0.982 25.84–36.34 2.00E+01 7.90E+01 -0.60 1.57 1.00E+04 -2.70
Cosavirus RNA+ ss Transcript RNA -3.16 ± 0.27 107% 0.978 24.26–31.41 1.00E+03 7.90E+01 1.10 1.35 1.00E+04 -1.00
Norovirus GGI RNA+ ss Transcript RNA -3.37 ± 0.28 98% 0.973 26.97–38.43 1.00E+02 7.90E+01 0.10 1.44 1.00E+03 -1.00
Norovirus GGIV RNA+ ss Transcript RNA -3.53 ± 0.35 92% 0.952 22.7–37.92 2.00E+03 7.90E+01 1.40 1.51 1.00E+03 0.30
Norovirus GGII RNA+ ss Transcript RNA -3.44 ± 0.32 95% 0.954 23.01–38.53 1.00E+02 7.90E+01 0.10 1.64 1.00E+03 -1.00
OC43 RNA+ ss Transcript RNA -3.39 ± 0.31 97% 0.952 22.84–37.70 1.00E+01 3.95E+02 -1.60 1.67 1.00E+04 -3.00
NL63 RNA+ ss Transcript RNA -3.31 ± 0.83 100% 0.851 28.59–36.63 2.00E+02 3.95E+02 -0.30 1.97 1.00E+04 -1.70
Hepatitis A virus RNA+ ss Transcript RNA -3.27 ± 0.46 102% 0.916 26.03–39.80 1.00E+02 3.95E+02 -0.60 2.14 1.00E+03 -1.00
Adenovirus 41 DNA ds Stool -3.00 ± 0.16 115% 0.986 23.43–35.08 1.00E+02 7.90E+01 0.10 1.47 1.00E+02 0.00
Astrovirus RNA+ ss Stool -3.65 ± 0.54 88% 0.943 32.88–42.23 2.00E+02 7.89E+03 -1.60 3.40 1.00E+05 -2.70
Rotavirus Wa RNA+ ds Cell production -3.51 ± 0.79 93% 0.812 22.05–36.45 1.00E+02 7.89E+02 -0.90 1.56 1.00E+04 -2.00
MNV-1 RNA+ ss Cell production -3.01 ± 0.32 115% 0.947 28.33–38.14 1.00E+02 3.95E+02 -0.60 1.95 1.00E+04 -2.00
Enterovirus RNA+ ss Cell production -3.36 ± 0.59 98% 0.894 25.28–36.79 1.00E+03 3.95E+02 0.40 1.97 1.00E+03 0.00
Mengovirus RNA+ ss Cell production -3.21 ± 0.20 105% 0.983 26.77–38.00 1.00E+02 7.89E+02 -0.90 2.05 1.00E+04 -2.00

a LOD expressed as number of genome copies/μl of nucleic acids.

b formula = [log10(OD)-log10(digital)].